Why does my 1990 Civic have a worsening chugging problem?

My car has been chugging, but sometimes it only chugs once and then drives okay for a while. Generally the chugging is bad enough to make the check engine light come on, but not to stop the car altogether. Sometimes it seems like it's worse in second gear than the others, and it usually improves if I drive at higher RPMs. I checked out the spark plugs and three were fine, but the fourth had a bit of oil on it and I replaced it with no change. It also has brand-new fuel and air filters. One guy looked at it for me and found a chunk of metal in the fuel line and that seemed to solve the problem at first, but the next day it started chugging again.